sars-cov-2-recovery 4.0

Added
-mapping final consenus with Minimap2 to SARS-CoV-2 reference sequence

Changed
-extract majority variant's list with SnpEff eff from the consensus mapped with minimap2 to fix a wrong classification of substitutions/deletion into the minority report when mapping detected a position in 49.9% of the sequencing reads.

Fixed

sars-cov-2-recovery 3.5

Added iVar trimming for Illumina

sars-cov-2-recovery 3.4

Added nextclade to the analysis pipeline

sars-cov-2-recovery 3.3

A private Galaxy cluster will be targeted eliminating the use of a token to avoid accidental use of the specific tools from the public ARIES server.

sars-cov-2-recovery 3.1

Input can be either Illumina, Ion Torrent or Nanopore fastq, either Sanger or consensus fasta.